There are no error messages associated with this issue. However, the behavior can be unexpected.
This behavior is by design and as expected. As long as a Mailbox archive is accessible, whether or not it's marked for deletion, it will require a license and the Usage Analyzer will count it as such.
Note: While a mailbox archive may not have its properties displayed or be searched from the Vault Admin Console, end users who have permissions are still able to search it and access it. This can be done from the client extensions on a mailbox.
To ensure mailbox archives are marked for deletion and are not counted as 'Actual Usage' by the Usage Analyzer, it will be necessary to zap the permissions on the archive.
Use Enterprise Vault Policy Manager (EVPM) to remove all the permissions from the archive as referenced in the following article:
How to remove all permissions from an archive using Enterprise Vault Policy Manager (EVPM)
Once this is complete, subsequent runs of the Usage Analyzer will no longer count the mailbox archive towards 'Actual Usage'.
There may be cases where archives stay perpetually in a 'Marked for Deletion' state. For example: If the storage partition that the archived data is stored on is a worm device or if the storage device manages it's own retention and the retention period has not expired. In such cases, attempts to run the Enterprise Vault Usage Analyzer will still count these archives as 'Actual Usage' and these archives will require sufficient licensing for Enterprise Vault.